How do you call `bpy.ops.clip.rebuild_proxy()` in the python api without getting a context is incorrect error
So it sounds like the problem is that the wrong part of the interface ('Area') is active at the moment you're calling ops.clip.rebuild_proxy() or sequencer.rebuild_proxy().

I'm working on an add-on that will allow me to add a movie strip, draw waveforms, and start a 50% proxy build all with a single action. I found that I had to iterate through the areas and override the context to rebuild proxy for a specific clip. Here's what worked for me: 

ctx = bpy.context.copy()
for area in bpy.context.screen.areas:
    if area.type == 'CLIP_EDITOR':
        ctx['area'] = area
        bpy.ops.clip.rebuild_proxy()